I am sure this is simple but I can't seem to figure this out. I know you can have multiple forums on the main page with sections underneath to help catgorize the page. But can you also have multiple sub forums with sections under it as well?

not quite sure i understand, but you can have multiple subforums within a forum, if you have the option in the ACP forums section for them to show in the list of the parent forum, the links to those subforums will be shown as seen in the red box in this image!